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To set up and run Space Ranger, follow these steps:
Space Ranger 4.0.1 (Jun 12, 2025)
- Visium Spatial Software Suite
- Self-contained, relocatable tar file. Does not require centralized installation.
- Contains binaries pre-compiled for CentOS/RedHat 7.0 and Ubuntu 16.04.
- Runs on Linux systems that meets the minimum compute requirements.
- View Space Ranger source code on GitHub
tar.gz compression
Download for Linux 64-bit (tar.gz)File size: 885 MBmd5sum: b0beb100947717cee8c7ad0d7a9f0247curlwgetcurl -o spaceranger-4.0.1.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-4.0.1.tar.gz?Expires=1765089543&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=UgvBv5~cbwh8a167T3ucOrUD-XUsiGhb8wYJY-Pl3-jD9wECNSw-EMj5klav7iqXG8mA4Dri62m6-Ym3JBLhC4mF2eNw8W20owE2YHgS7na8gxsbfsvJMNVRzY8ziNroBV7VkSH6bNoGeMFPyhetUa~yx9UCrUcvjYMirKTr6bAKuOFgPrLCVN2LoisHPvM0Yhgz-chpAWREYBGv4hH70W0eyEYcrCbgv10~oPASS5WwgkH9Jf9UT6HavLCn0S2k9mcG4VxAuDI29ejwjWoVOz2RIAT4d4ti5HF-IlJ~I4ZBRFP7dWqNwtUrJkOWQcO-f-dx2HuP8TrRr3FsAE32iw__"tar.xz compression
Download for Linux 64-bit (tar.xz)File size: 582 MBmd5sum: 3610ff948a6f8129cf49509f1bb34970curlwgetcurl -o spaceranger-4.0.1.tar.xz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-4.0.1.tar.xz?Expires=1765089543&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=euOw6OwtN4z2wsCmzIXqVteEtcSlYk1h2GK9-v5D5oU9JwaEbpRIH~ncgo8cz06SjSGyV2lWww-7AVtlOq~h5VjzcqbK9IqH07ofzLqemJYanyb7NyIdx4zlQSCSErbVAlEfNYjTbq5qUP-MsCGFHGMUS2fhb-F8MNDOz9Cfbf8tOYmjOmcwpcwVyxbww8UZUEjdt4Q2NcEkPH3JX-te4FBs4sEQg4WWrBSRaQRasxDy24czVNcHutZOi9tNzNqMtDkvLziuyFmS3Sz9xuEqV2ku1jVvrMlranXVjY65BM89MYbUpp0tJS~fY7BEt2363hZr0ma-lAARXKBBJG1Q4w__"
Download is unavailable on mobile devices.
Space Ranger v4.0.1 highlights
- Space Ranger v4.0 now supports Visium HD 3' Gene Expression!
- Cell and nucleus segmentation are now included for Visium HD and Visium HD 3' data with H&E images.
- Space Ranger v4.0 now features a new UMI-based registration algorithm for Visium HD and Visium HD 3' data.
- Starting with v4.0, anonymized telemetry data is collected and sent to 10x Genomics.
References
10x Genomics offers pre-built human and mouse references for download. You can alternatively create a custom reference.
Human reference (GRCh38) - 2024-A
- Human reference (GRCh38)
Download Human ReferenceFile size: 11 GBmd5sum: a7b5b7ceefe10e435719edc1a8b8b2facurlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz"Mouse reference (GRCm39) - 2024-A
- Mouse reference (GRCm39)
Download Mouse ReferenceFile size: 9.7 GBmd5sum: 37c51137ccaeabd4d151f80dc86ce0b3curlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCm39-2024-A.tar.gz"Rat reference (mRatBN7.2) - 2024-A
- Rat reference (mRatBN7.2)
Download Rat ReferenceFile size: 9.5 GBmd5sum: 34d4af0874a45dfa03436efe4eaec2fecurlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mRatBN7-2-2024-A.tar.gz"Human (GRCh38) and mouse (GRCm39) reference - 2024-A
- Human (GRCh38) and mouse (GRCm39) reference
Download Human + Mouse ReferenceFile size: 11 GBmd5sum: b2d628e6c6813e1396989a9a9ca2ef23curlwgetcurl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38_and_GRCm39-2024-A.tar.gz"
Download is unavailable on mobile devices.
Probe Sets
Visium probe-based assays target genes in the human or mouse transcriptomes. For these assays, it is required to specify the relevant probe set to the View more details about probe setsspaceranger count pipeline. Probe sets come bundled with the Space Ranger package and are also available for download here for convenience.
Human Transcriptome v2.1
- Probe Set CSV v2.1
Pair with the GRCh38 (2024-A) reference
- Probe Set BED v2.1
- Possible Off-Target Probes CSV v2.1
- Probe Set Metadata TSV v2.1
Human Transcriptome v2
- Probe Set CSV v2
Pair with the GRCh38 (2020-A) reference
- Probe Set BED v2
- Possible Off-Target Probes CSV v2
- Probe Set Metadata TSV v2
- Probe Set Metadata Excel Spreadsheet v2
Human Transcriptome v1
- Probe Set CSV v1
Pair with the GRCh38 (2020-A) reference
- Probe Set BED v1
- Possible Off-Target Probes CSV v1
- Probe Set Metadata TSV v1
- Probe Set Metadata Excel Spreadsheet v1
Mouse Transcriptome v2.1
- Probe Set CSV v2.1
Pair with the GRCm39 (2024-A) reference
- Probe Set BED v2.1
- Possible Off-Target Probes CSV v2.1
- Probe Set Metadata TSV v2.1
Mouse Transcriptome v2
- Probe Set CSV v2
Pair with the mm10 (2020-A) reference
- Probe Set BED v2
- Possible Off-Target Probes CSV v2
- Probe Set Metadata TSV v2
- Probe Set Metadata Excel Spreadsheet v2
Mouse Transcriptome v1
- Probe Set CSV v1
Pair with the mm10 (2020-A) reference
- Probe Set BED v1
- Possible Off-Target Probes CSV v1
- Probe Set Metadata TSV v1
- Probe Set Metadata Excel Spreadsheet v1
Slide File Download
If Space Ranger is to be run in an environment without access to the Internet, the pipeline will require a Visium slide layout file using the --slidefile option. Enter the slide serial number below to download the corresponding slide layout file.
Other downloads
Feature Reference CSV Files
System requirements
View the minimum requirements to run Space Ranger pipelines
Installation
View instructions on how to install Space Ranger